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BioC 3.4: CHECK report for LOBSTAHS on morelia

This page was generated on 2016-09-21 03:56:08 -0700 (Wed, 21 Sep 2016).

Package 661/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LOBSTAHS 0.99.8
James Collins
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LOBSTAHS
Last Changed Rev: 119439 / Revision: 121152
Last Changed Date: 2016-07-18 11:35:31 -0700 (Mon, 18 Jul 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: LOBSTAHS
Version: 0.99.8
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOBSTAHS_0.99.8.tar.gz
StartedAt: 2016-09-20 08:33:04 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 08:34:49 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 105.1 seconds
RetCode: 0
Status:  OK 
CheckDir: LOBSTAHS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings LOBSTAHS_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/LOBSTAHS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LOBSTAHS/DESCRIPTION’ ... OK
* this is package ‘LOBSTAHS’ version ‘0.99.8’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LOBSTAHS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
loadLOBdbase 8.623  0.094   8.723
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/LOBSTAHS.Rcheck/00check.log’
for details.


LOBSTAHS.Rcheck/00install.out:

* installing *source* package ‘LOBSTAHS’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LOBSTAHS)

LOBSTAHS.Rcheck/LOBSTAHS-Ex.timings:

nameusersystemelapsed
LOBSet-class0.0020.0000.002
LOBSet0.0020.0000.003
LOBdbase-class0.0020.0000.002
LOBdbase0.0030.0010.004
doLOBscreen2.0200.0942.143
extractLOBdbasedata0.4550.0240.479
generateLOBdbase0.0000.0000.001
getLOBpeaklist0.0370.0010.037
loadLOBdbase8.6230.0948.723